Fluorine in PDB 7ude: Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K

Enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K, PDB code: 7ude was solved by B.V.Plapp, L.Gakhar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.28, 51.18, 92.59, 91.9, 103.02, 109.89
R / Rfree (%) 13.3 / 16

Other elements in 7ude:

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K (pdb code 7ude). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K, PDB code: 7ude:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7ude

Go back to Fluorine Binding Sites List in 7ude
Fluorine binding site 1 out of 6 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:17.1
occ:1.00
 F1 A:ETF404 0.0 17.1 1.0
C1 A:ETF404 1.4 14.2 1.0
F3 A:ETF404 2.1 17.0 1.0
F2 A:ETF404 2.3 16.8 1.0
C2 A:ETF404 2.3 11.9 1.0
O A:ETF404 2.9 10.4 1.0
CG2 A:VAL294 3.2 9.6 0.6
C3N A:NAJ403 3.2 8.4 1.0
C2N A:NAJ403 3.3 8.3 1.0
OG A:SER48 3.3 9.8 1.0
CG2 A:VAL294 3.4 11.2 0.4
C7N A:NAJ403 3.6 8.7 1.0
C4N A:NAJ403 3.7 9.3 1.0
N1N A:NAJ403 3.8 8.3 1.0
O7N A:NAJ403 3.9 8.9 1.0
CB A:SER48 4.2 8.9 1.0
C5N A:NAJ403 4.3 9.2 1.0
N7N A:NAJ403 4.3 8.9 1.0
C6N A:NAJ403 4.3 9.0 1.0
O2D A:NAJ403 4.5 9.7 1.0
C1D A:NAJ403 4.7 8.9 1.0
CB A:VAL294 4.7 10.2 0.6
CB A:VAL294 4.8 10.7 0.4
ZN A:ZN401 4.8 10.4 1.0
CE1 A:PHE93 5.0 9.6 1.0

Fluorine binding site 2 out of 6 in 7ude

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Fluorine binding site 2 out of 6 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:16.8
occ:1.00
 F2 A:ETF404 0.0 16.8 1.0
C1 A:ETF404 1.4 14.2 1.0
F3 A:ETF404 2.1 17.0 1.0
F1 A:ETF404 2.3 17.1 1.0
C2 A:ETF404 2.3 11.9 1.0
CE1 A:PHE93 3.2 9.6 1.0
O A:ETF404 3.6 10.4 1.0
CD1 A:PHE93 3.7 9.4 1.0
CD2 A:LEU116 3.8 19.3 1.0
CZ A:PHE93 3.9 10.2 1.0
CD1 A:LEU116 4.0 18.6 1.0
CD1 A:LEU141 4.1 13.3 1.0
O7N A:NAJ403 4.4 8.9 1.0
CG A:LEU116 4.5 15.5 1.0
CG2 A:ILE318 4.7 10.3 1.0
C7N A:NAJ403 4.7 8.7 1.0
CG A:PHE93 4.8 9.1 1.0
C3N A:NAJ403 4.8 8.4 1.0
OG A:SER48 4.8 9.8 1.0
CE2 A:PHE93 4.9 10.4 1.0
C4N A:NAJ403 4.9 9.3 1.0

Fluorine binding site 3 out of 6 in 7ude

Go back to Fluorine Binding Sites List in 7ude
Fluorine binding site 3 out of 6 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:17.0
occ:1.00
 F3 A:ETF404 0.0 17.0 1.0
C1 A:ETF404 1.3 14.2 1.0
F1 A:ETF404 2.1 17.1 1.0
F2 A:ETF404 2.1 16.8 1.0
C2 A:ETF404 2.3 11.9 1.0
O A:ETF404 2.9 10.4 1.0
OG A:SER48 3.1 9.8 1.0
CB A:SER48 3.2 8.9 1.0
CD1 A:LEU57 3.7 13.1 0.3
CD2 A:LEU57 4.0 14.3 0.7
CG2 A:VAL294 4.1 9.6 0.6
CD1 A:LEU141 4.3 13.3 1.0
CD1 A:LEU116 4.4 18.6 1.0
CG2 A:VAL294 4.6 11.2 0.4
CA A:SER48 4.6 9.3 1.0
ZN A:ZN401 4.6 10.4 1.0
NE2 A:HIS67 4.7 10.2 1.0

Fluorine binding site 4 out of 6 in 7ude

Go back to Fluorine Binding Sites List in 7ude
Fluorine binding site 4 out of 6 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:21.4
occ:1.00
 F1 B:ETF404 0.0 21.4 1.0
C1 B:ETF404 1.4 17.4 1.0
F3 B:ETF404 2.1 19.8 1.0
F2 B:ETF404 2.2 20.2 1.0
C2 B:ETF404 2.4 14.5 1.0
O B:ETF404 2.9 13.4 1.0
CG2 B:VAL294 3.1 13.7 0.5
C3N B:NAJ403 3.2 10.2 1.0
C2N B:NAJ403 3.3 10.7 1.0
OG B:SER48 3.3 12.1 1.0
C7N B:NAJ403 3.6 10.7 1.0
CG2 B:VAL294 3.6 13.3 0.5
C4N B:NAJ403 3.7 11.8 1.0
N1N B:NAJ403 3.8 10.7 1.0
O7N B:NAJ403 3.9 11.2 1.0
CB B:SER48 4.2 11.2 1.0
C5N B:NAJ403 4.3 11.0 1.0
N7N B:NAJ403 4.3 11.3 1.0
C6N B:NAJ403 4.3 10.5 1.0
CB B:VAL294 4.5 12.5 0.5
O2D B:NAJ403 4.6 12.0 1.0
C1D B:NAJ403 4.7 10.8 1.0
ZN B:ZN401 4.8 13.2 1.0
CE1 B:PHE93 5.0 12.4 1.0
CB B:VAL294 5.0 12.1 0.5

Fluorine binding site 5 out of 6 in 7ude

Go back to Fluorine Binding Sites List in 7ude
Fluorine binding site 5 out of 6 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:20.2
occ:1.00
 F2 B:ETF404 0.0 20.2 1.0
C1 B:ETF404 1.3 17.4 1.0
F3 B:ETF404 2.1 19.8 1.0
F1 B:ETF404 2.2 21.4 1.0
C2 B:ETF404 2.3 14.5 1.0
CE1 B:PHE93 3.3 12.4 1.0
O B:ETF404 3.6 13.4 1.0
CD2 B:LEU116 3.8 22.1 1.0
CD1 B:PHE93 3.8 12.1 1.0
CZ B:PHE93 4.0 12.8 1.0
CD1 B:LEU116 4.1 22.0 1.0
CD1 B:LEU141 4.2 17.3 1.0
O7N B:NAJ403 4.3 11.2 1.0
CG B:LEU116 4.6 19.0 1.0
CG2 B:ILE318 4.7 13.2 1.0
C7N B:NAJ403 4.7 10.7 1.0
C3N B:NAJ403 4.7 10.2 1.0
OG B:SER48 4.8 12.1 1.0
CG B:PHE93 4.8 11.6 1.0
CD1 B:ILE318 4.9 16.5 1.0
C4N B:NAJ403 4.9 11.8 1.0
CG2 B:VAL294 4.9 13.7 0.5
CE2 B:PHE93 4.9 12.2 1.0

Fluorine binding site 6 out of 6 in 7ude

Go back to Fluorine Binding Sites List in 7ude
Fluorine binding site 6 out of 6 in the Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Horse Liver Alcohol Dehydrogenase with Nad and Trifluoroethanol at 125 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:19.8
occ:1.00
 F3 B:ETF404 0.0 19.8 1.0
C1 B:ETF404 1.3 17.4 1.0
F1 B:ETF404 2.1 21.4 1.0
F2 B:ETF404 2.1 20.2 1.0
C2 B:ETF404 2.4 14.5 1.0
O B:ETF404 2.8 13.4 1.0
OG B:SER48 3.1 12.1 1.0
CB B:SER48 3.2 11.2 1.0
CG2 B:VAL294 4.1 13.7 0.5
CD2 B:LEU57 4.1 22.6 1.0
CD1 B:LEU141 4.3 17.3 1.0
CD1 B:LEU116 4.5 22.0 1.0
CA B:SER48 4.6 12.0 1.0
CG2 B:VAL294 4.6 13.3 0.5
ZN B:ZN401 4.6 13.2 1.0
NE2 B:HIS67 4.7 13.1 1.0

Reference:

B.V.Plapp, L.Gakhar, R.Subramanian. Dependence of Crystallographic Atomic Displacement Factors on Temperature (25-150 K) For Complexes of Horse Liver Alcohol Dehydrogenases Acta Crystallogr.,Sect.D V. D78 1221 2022.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798322008361
Page generated: Fri Aug 2 14:05:42 2024

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